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You can edit the color scheme settings file found in data/init/colors.txt. The file is fairly self explanatory - DF uses 16 color different colors, and each of those colors are further split into RGB channels when setting the colors. Before modifying this file, it is a good idea to make a backup of it.

MagmaWiki has a comprehensive list of examples where each color is used, as well as examples of alternative color schemes you can use on the color scheme article.